anvi-export-collection

Export a collection from an anvi'o database.

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Authors

A. Murat Eren (Meren)
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Requires

profile-db

Can use

pan-graph-db collection

Provides

collection-txt

Usage

This program, as one might think, allows you to export a collection. This allows you to take your binning results elsewhere (including into another Anvi’o project with the command anvi-import-collection).

You can run this program on a profile-db or pan-db as follows:

anvi-export-collection -C my_favorite_collection \ -p profile-db

This will give you a collection-txt file that describes the collection my_favorite_collection.

To list the collections available in this database, you can run

anvi-export-collection -p pan-db \ --list-colllections

You can also add the flag --include-unbinned to have all unbinned contigs in the database show up at the end of your collection-txt file in a bin titled UNBINNED.

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-export-collection.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-export-collection [-h] -p PAN_OR_PROFILE_DB [-C COLLECTION_NAME] [-O FILENAME_PREFIX] [--list-collections] [--include-unbinned]

Parameters and their descriptions

options
-p, --pan-or-profile-db PAN_OR_PROFILE_DB required
An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-C, --collection-name COLLECTION_NAME
Collection name.
-O, --output-file-prefix FILENAME_PREFIX
A prefix to be used while naming the output files. No file type extensions please; just a prefix -- all ouptut file names and extensions will be appended to this prefix.
--list-collections
Show available collections and exit.
--include-unbinned
When this flag is used, anvi'o will also store in the output file the items that do not appear in any of your bins. This new bin will be called 'UNBINNED_ITEMS_BIN'. Yes. The ugly name is intentional.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.

Copyleft, The anvi'o Project